The plot goes that Phineas, Ferb and their friends are literally space surfing along a meteor shower and head back to their customized space station. At the same time Perry is battling Doofenshmirtz as per usual and breaks up his latest -inator which coincidentally happens to take away superpowers. In the midst of their battle, a stray shot manages to fire off before the machine is destroyed. And yet again at the same time in New York, Spider-Man, Hulk, Iron Man and Thor are battling against Red Skull, Venom, Whiplash and M.O.D.O.K.. Just as they're about to beat them, the ray bounces off the space station and onto the heroes, taking away their powers and allowing the villains to escape.

After the heroes regroup on the S.H.I.E.L.D carrier, Nick Fury manages to track the ray back to Danville and Phineas and Ferb's house. So the four heroes head to the pair in hopes they can restore their powers. At the same time, the villains likewise manage to track the source of the ray to Doofenshmirtz (thanks to Doofenshmirtz bragging about it on the internet) in the hopes of gaining the heroes' powers for themselves.

Can Phineas and Ferb save the day? Or will the villains actually take advantage of this opportunity and manage to take over the world?

Perry in a superhero garb saves the heroes in their second fight against the villains.

Hulkjeet, Phineas and Ferb, Perry, and Doofenshmirtz arrive to help the captured superheroes before the penultimate battle. Candace and Isabella likewise do this at the end by unwittingly stopping Red Skull before he can activate his device and restoring the heroes' powers.

Doofenshmirtz brings up the fact that he once tried MODOK's look once but found it difficult to maneuver through doors. Later, MODOK has trouble fitting through one of Doof's doors.

Brought Down to Badass: Once the superheroes get some help from Phineas and Ferb and their friends and a chance to exercise their ingenuity, they put up a pretty good fight against the villains even without their powers.

Eyepatch of Power: Spoofed with Major Monogram when Fury is briefing Perry on what's happening. Fury notices he suddenly has a eyepatch but Monogram claims its a medical issue. Though Carl quickly points out he's trying to look cool. One cutaway later and Monogram has two of them on.

Face Palm: Nick Fury does one after dealing with Major Monogram, and Red Skull later does the same in response to Doofenshmirtz.

Fangirl: Candace turns out to be a major one of superheroes. Who knew.

Fantastic Racism: Red Skull apparently hates people from Drusselstein. Which makes sense; the guy's a Nazi.

Grievous Harm with a Body: During the ending battle, Thor and The Hulk play a short game of badminton....with Venom in place as the shuttlecock.

Holding Back the Phlebotinum: Doofenshmirtz's disintegrator-inator could have easily saved the day, but Doofenshmirtz doesn't even remember that it exists until halfway through the climax, and the conflict is resolved by the time he plugs it in.

Hulking Out: The Hulk himself is perpetually seen in his Hulked-out state, even after he loses his powers. Played straighter though by Baljeet after he is accidentally hit by gamma rays.

Insane Troll Logic: Candace uses this to determine the proper way to release the superheroes' trapped powers.

Jerkass Ball: Phineas has never been shown to be as short-tempered and harsh as he is in this special. A little justified though as he's under pressure with the world at stake and all. He goes back to normal at the end of everything.

Keep Away: The penultimate battle consists of the good guys using everything they have to keep the villains from obtaining the reactor core that powers their destructive machine. The villains do retrieve the reactor core eventually, but it goes on long enough for Candace and Isabella to bring back the superheroes' lost powers.

Knight of Cerebus: Red Skull is by far, the most dangerous villain to enter Phineas and Ferb's setting.

Lampshade Hanging: Isabella comments to Candace how detached they are to helping the heroes because "the female heroes didn't show up."

Multi Layer Facade: When Buford tries unmasking the mysterious platypus superhero, his secret identity turns out to be...Ducky Momo. Then Perry shows up, and we see a Ducky Momo mask discarded in a nearby trash can.

Mysterious Protector: Perry shows up at several points to aid the heroes without any of them knowing his true identity. To a lesser extent, Doofenshmirtz. The heroes have no idea who he is when he joins the fight against the villains.

Nice Job Breaking It, Hero!: Candace twice when she prematurely activates Phineas and Ferb devices to restore the heroes' powers. The first time it mixes up the power, the second time they wind up hitting the wrong person. Her second slip-up does pay off though during the penultimate battle.

Non-Standard Character Design: The Marvel superheroes and supervillains stand out sharply when side-by-side with the Phineas and Ferb characters.

O.O.C. Is Serious Business: You know the stakes are high when Phineas snaps not once, but twice. It's especially notable in that this is probably the one time in the show's history that Phineas is actually aware of the full gravity of the situation he's in.

It takes a while for Doofenshmirtz (beingDoofenshmirtz) to remember that he could simply use his disintegrator-inator to defeat the supervillains. He then gets sidetracked trying to find a long enough extension cord to power the inator and only activates it after the battle is over, in time to vanish Phineas and Ferb's crashed space station. It took time until he found a cord as long as needed or realized a longer cord would do.

For some reason, Perry doesn't use the wire cutters he had with him all along to break him and Doofenshmirtz out of the cages they are trapped inside until Doofenshmirtz asks him whether he has any powers to help them escape. Waiting a while to escape the trap seems to be OWCA standard procedure.

Some Marvel characters who don't appear still get referenced, including Ghost Rider, Aunt May and — of all characters — Howard the Duck.

Doofenshmirtz trying to prove himself worthy of joining Red Skull, only for the latter to abandon him because of his sheer incompetence is reminiscent of Justin Hammer's attempts to impress Red Skull in Avengers Assemble. What adds to this parallel is that both Doofenshmirtz and Justin Hammer are scientists.

Third Time's the Charm: Candace reasons that since she has failed twice already, she won't screw up a third time. This at first seems like Wrong Genre Savviness when the space station shuts down, but it turns out to be exactly what's needed to halt the villains and restore the superheroes' powers.

Title-Only Opening: This episode doesn't play the title theme, just Phineas and Ferb rocking out on guitars as the title comes up from the ground. With Spider-Man taking over Candace's role.

Worf Had the Flu: The lack of (or, at one point, switched) superpowers leads to the superheroes being curbstomped several times. In addition, Phineas and Ferb's new Beak suit is only partly functional and is broken in both of the battles it is involved in.

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